Add the clams to a large skillet. Cover with a lid and heat over medium-high heat. Steam for 3 minutes, and then remove the lid and transfer all opened clams to a bowl to cool. Cover the skillet and cook again for 1 to 2 minutes more. Remove the lid and again transfer all opened clams to the bowl. Repeat another time, if necessary, until most clams have opened. Discard any clams that do not open.
Pour the broth from the skillet into another bowl and set aside. Once cool enough to handle, remove the meat from three-quarters of the opened clams and chop the meat finely. Discard their shells. Try to capture any of the juice and combine with the reserved broth.
Add the spaghetti to the boiling water and cook until al dente, 1 minute less than the package instructions call for.
In the same large skillet the clams were cooked in, add the olive oil and heat until hot. Saute the chili flakes and garlic. As soon as the garlic is fragrant, add the white wine and cook until reduced, about 3 minutes.
Add the chopped clams along with the clams still in their shells to the skillet with some of the reserved juices (about 1/2 cup). Cook until reduced slightly, and then season with salt and pepper. Toss together thoroughly.
Drain the spaghetti and add to the sauce. Toss over high heat for a few moments until the pasta is well coated.
Serve the dressed pasta with the chopped parsley, a drizzle of olive oil and an extra touch of crushed chili flakes.